Damage to the DNA sequence can evade DNA repair pathways, such as Base Excision Repair (BER), and the enzymes that initiate this process, like Thymine DNA Glycosylase (TDG). DNA lesions, such as thymine in the place of a cytosine, can then be replicated to produce mutations. These mutations can then lead to many different illnesses, including cancer. Understanding how repair enzymes recognize lesions, a step that is not well understood, can be vitally important in the prevention of these diseases. Local conformational properties of the two primary conformations of the DNA backbone near the lesion site could be a reason the enzyme recognizes the lesion. 31P chemical shift assignments can be used to quantify the percent BI and BII conformational states of the DNA backbone. To best understand this process, sample conditions should reflect cellular conditions. This project analyzes the impact the sample conditions have on the energetics and local conformational properties. The differing sample conditions were used on palindromic dodecamer sequences: the Drew Dickerson Dodecamer as the control, and the same sequence containing a T:G mismatch as a comparison to analyze the impact sample conditions has on the backbone conformational dynamics and energetics of a lesioned sequence, using 1D 31P solution NMR experiments. These sample conditions range from introducing different ions, ionic strength, concentration of ions, and more.

Influence of sample conditions on DNA backbone conformation equilibrium using 31P solution NMR

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